Starting phenix.real_space_refine on Sat Jun 21 00:48:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dch_46751/06_2025/9dch_46751.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dch_46751/06_2025/9dch_46751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dch_46751/06_2025/9dch_46751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dch_46751/06_2025/9dch_46751.map" model { file = "/net/cci-nas-00/data/ceres_data/9dch_46751/06_2025/9dch_46751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dch_46751/06_2025/9dch_46751.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 14 6.06 5 P 10 5.49 5 S 106 5.16 5 C 15367 2.51 5 N 4476 2.21 5 O 4460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24433 Number of models: 1 Model: "" Number of chains: 15 Chain: "G" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 219 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3124 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain breaks: 4 Unresolved non-hydrogen bonds: 589 Unresolved non-hydrogen angles: 737 Unresolved non-hydrogen dihedrals: 473 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 11, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 377 Chain: "B" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 2786 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 17, 'TRANS': 405} Chain breaks: 9 Unresolved non-hydrogen bonds: 751 Unresolved non-hydrogen angles: 937 Unresolved non-hydrogen dihedrals: 602 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 13, 'TYR:plan': 3, 'ASN:plan1': 11, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 407 Chain: "D" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2715 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 520 Unresolved non-hydrogen angles: 665 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 17, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 22, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 286 Chain: "F" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 695 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 95 Chain: "E" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 187 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2589 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 12, 'TRANS': 352} Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 15, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 189 Chain: "H" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3128 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain breaks: 4 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 470 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 11, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 373 Chain: "I" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 2789 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'PTRANS': 17, 'TRANS': 405} Chain breaks: 9 Unresolved non-hydrogen bonds: 748 Unresolved non-hydrogen angles: 933 Unresolved non-hydrogen dihedrals: 600 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 13, 'TYR:plan': 3, 'ASN:plan1': 11, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 407 Chain: "K" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2718 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 517 Unresolved non-hydrogen angles: 661 Unresolved non-hydrogen dihedrals: 403 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 17, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 22, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 286 Chain: "M" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 695 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 95 Chain: "L" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 187 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "J" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2587 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 12, 'TRANS': 352} Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 15, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 189 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1873 SG CYS A 528 46.993 69.401 121.243 1.00 55.10 S ATOM 1918 SG CYS A 535 45.606 72.727 119.808 1.00 62.62 S ATOM 1941 SG CYS A 539 44.918 71.787 123.440 1.00 59.67 S ATOM 1873 SG CYS A 528 46.993 69.401 121.243 1.00 55.10 S ATOM 1954 SG CYS A 541 48.289 70.681 124.577 1.00 55.84 S ATOM 2006 SG CYS A 548 49.096 72.553 121.388 1.00 49.70 S ATOM 2041 SG CYS A 552 50.640 69.065 122.045 1.00 46.34 S ATOM 1918 SG CYS A 535 45.606 72.727 119.808 1.00 62.62 S ATOM 2006 SG CYS A 548 49.096 72.553 121.388 1.00 49.70 S ATOM 2052 SG CYS A 554 48.564 71.296 117.849 1.00 53.75 S ATOM 2075 SG CYS A 558 48.321 75.042 118.622 1.00 51.10 S ATOM 2121 SG CYS A 565 65.591 78.651 121.173 1.00 30.93 S ATOM 2138 SG CYS A 567 68.433 81.182 120.595 1.00 27.67 S ATOM 2167 SG CYS A 571 68.626 78.576 123.543 1.00 26.53 S ATOM 2206 SG CYS A 576 66.094 80.796 123.980 1.00 27.85 S ATOM 2167 SG CYS A 571 68.626 78.576 123.543 1.00 26.53 S ATOM 2277 SG CYS A 585 66.799 75.438 122.710 1.00 26.69 S ATOM 2329 SG CYS A 593 69.495 76.948 120.415 1.00 25.83 S ATOM 2403 SG CYS A 606 70.627 75.206 123.514 1.00 26.71 S ATOM 2121 SG CYS A 565 65.591 78.651 121.173 1.00 30.93 S ATOM 2219 SG CYS A 578 63.539 77.427 123.738 1.00 24.36 S ATOM 2277 SG CYS A 585 66.799 75.438 122.710 1.00 26.69 S ATOM 2308 SG CYS A 590 63.979 75.513 120.185 1.00 25.92 S ATOM 1096 SG CYS A 286 56.179 56.338 126.316 1.00 46.75 S ATOM 1118 SG CYS A 289 59.849 57.367 126.174 1.00 43.23 S ATOM 1160 SG CYS A 294 58.933 54.356 128.288 1.00 44.98 S ATOM 13973 SG CYS H 528 63.182 104.059 132.419 1.00 82.67 S ATOM 14018 SG CYS H 535 63.029 101.105 134.898 1.00 92.88 S ATOM 14041 SG CYS H 539 59.829 102.719 133.619 1.00 84.19 S ATOM 13973 SG CYS H 528 63.182 104.059 132.419 1.00 82.67 S ATOM 14054 SG CYS H 541 60.414 103.065 129.991 1.00 78.74 S ATOM 14106 SG CYS H 548 62.978 100.513 131.086 1.00 66.72 S ATOM 14141 SG CYS H 552 64.125 103.397 128.866 1.00 72.26 S ATOM 14018 SG CYS H 535 63.029 101.105 134.898 1.00 92.88 S ATOM 14106 SG CYS H 548 62.978 100.513 131.086 1.00 66.72 S ATOM 14152 SG CYS H 554 66.291 101.180 132.939 1.00 88.37 S ATOM 14175 SG CYS H 558 64.349 97.935 133.520 1.00 77.43 S ATOM 14221 SG CYS H 565 66.446 89.474 117.562 1.00 50.77 S ATOM 14238 SG CYS H 567 67.022 87.319 115.521 1.00 44.28 S ATOM 14267 SG CYS H 571 64.814 89.851 113.910 1.00 40.04 S ATOM 14306 SG CYS H 576 65.201 86.235 115.851 1.00 45.78 S ATOM 14267 SG CYS H 571 64.814 89.851 113.910 1.00 40.04 S ATOM 14377 SG CYS H 585 66.076 92.799 115.604 1.00 44.94 S ATOM 14429 SG CYS H 593 68.590 90.301 114.155 1.00 40.20 S ATOM 14503 SG CYS H 606 66.632 92.485 111.781 1.00 38.41 S ATOM 14221 SG CYS H 565 66.446 89.474 117.562 1.00 50.77 S ATOM 14319 SG CYS H 578 63.947 91.825 118.590 1.00 41.82 S ATOM 14377 SG CYS H 585 66.076 92.799 115.604 1.00 44.94 S ATOM 14408 SG CYS H 590 67.892 92.735 118.843 1.00 44.31 S ATOM 13192 SG CYS H 286 64.997 114.188 121.132 1.00 78.21 S ATOM 13214 SG CYS H 289 66.234 114.137 117.487 1.00 70.41 S ATOM 13256 SG CYS H 294 63.428 116.535 118.535 1.00 64.74 S Residues with excluded nonbonded symmetry interactions: 14 residue: pdb="ZN ZN A 801 " occ=0.00 residue: pdb="ZN ZN A 802 " occ=0.58 residue: pdb="ZN ZN A 803 " occ=0.10 residue: pdb="ZN ZN A 804 " occ=0.14 residue: pdb="ZN ZN A 805 " occ=0.71 residue: pdb="ZN ZN A 806 " occ=0.00 residue: pdb="ZN ZN A 807 " occ=0.11 residue: pdb="ZN ZN H 801 " occ=0.00 residue: pdb="ZN ZN H 802 " occ=0.17 residue: pdb="ZN ZN H 803 " occ=0.32 residue: pdb="ZN ZN H 804 " occ=0.74 residue: pdb="ZN ZN H 805 " occ=0.37 ... (remaining 2 not shown) Time building chain proxies: 16.41, per 1000 atoms: 0.67 Number of scatterers: 24433 At special positions: 0 Unit cell: (157.14, 177.51, 212.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 14 29.99 S 106 16.00 P 10 15.00 O 4460 8.00 N 4476 7.00 C 15367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 457 " distance=2.03 Simple disulfide: pdb=" SG CYS H 325 " - pdb=" SG CYS H 457 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 530 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 539 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 535 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 528 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 528 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 541 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 548 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 552 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 535 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 558 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 554 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 548 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 571 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 565 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 567 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 576 " pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 593 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 571 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 585 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 606 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 565 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 585 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 590 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 578 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" ND1 HIS A 297 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 289 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 294 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 286 " pdb=" ZN H 801 " pdb="ZN ZN H 801 " - pdb=" NE2 HIS H 530 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 539 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 535 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 528 " pdb=" ZN H 802 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 528 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 548 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 552 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 541 " pdb=" ZN H 803 " pdb="ZN ZN H 803 " - pdb=" SG CYS H 535 " pdb="ZN ZN H 803 " - pdb=" SG CYS H 558 " pdb="ZN ZN H 803 " - pdb=" SG CYS H 554 " pdb="ZN ZN H 803 " - pdb=" SG CYS H 548 " pdb=" ZN H 804 " pdb="ZN ZN H 804 " - pdb=" SG CYS H 567 " pdb="ZN ZN H 804 " - pdb=" SG CYS H 571 " pdb="ZN ZN H 804 " - pdb=" SG CYS H 565 " pdb="ZN ZN H 804 " - pdb=" SG CYS H 576 " pdb=" ZN H 805 " pdb="ZN ZN H 805 " - pdb=" SG CYS H 585 " pdb="ZN ZN H 805 " - pdb=" SG CYS H 593 " pdb="ZN ZN H 805 " - pdb=" SG CYS H 571 " pdb="ZN ZN H 805 " - pdb=" SG CYS H 606 " pdb=" ZN H 806 " pdb="ZN ZN H 806 " - pdb=" SG CYS H 565 " pdb="ZN ZN H 806 " - pdb=" SG CYS H 585 " pdb="ZN ZN H 806 " - pdb=" SG CYS H 578 " pdb="ZN ZN H 806 " - pdb=" SG CYS H 590 " pdb=" ZN H 807 " pdb="ZN ZN H 807 " - pdb=" ND1 HIS H 297 " pdb="ZN ZN H 807 " - pdb=" SG CYS H 294 " pdb="ZN ZN H 807 " - pdb=" SG CYS H 289 " pdb="ZN ZN H 807 " - pdb=" SG CYS H 286 " Number of angles added : 72 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6876 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 49 sheets defined 22.0% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 22 through 61 Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.567A pdb=" N THR A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 284' Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.861A pdb=" N THR A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 652 through 665 Processing helix chain 'A' and resid 687 through 691 removed outlier: 3.802A pdb=" N PHE A 691 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 107 Proline residue: B 93 - end of helix removed outlier: 3.553A pdb=" N ARG B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.786A pdb=" N LYS B 465 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 removed outlier: 3.723A pdb=" N HIS B 507 " --> pdb=" O GLN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.837A pdb=" N PHE B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 602 Processing helix chain 'B' and resid 607 through 625 Processing helix chain 'B' and resid 628 through 643 removed outlier: 4.030A pdb=" N ASN B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 639 " --> pdb=" O ALA B 635 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL B 640 " --> pdb=" O CYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 651 Processing helix chain 'B' and resid 652 through 662 Processing helix chain 'B' and resid 663 through 667 removed outlier: 3.567A pdb=" N ASN B 667 " --> pdb=" O HIS B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 689 removed outlier: 3.571A pdb=" N GLU B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 27 removed outlier: 3.790A pdb=" N LYS D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'F' and resid 193 through 210 removed outlier: 4.097A pdb=" N ALA F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 262 Processing helix chain 'F' and resid 276 through 281 removed outlier: 3.645A pdb=" N ASP F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 292 removed outlier: 3.917A pdb=" N LYS F 291 " --> pdb=" O MET F 288 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG F 292 " --> pdb=" O PRO F 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 288 through 292' Processing helix chain 'E' and resid 142 through 148 removed outlier: 3.723A pdb=" N ASP E 146 " --> pdb=" O THR E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.765A pdb=" N ARG E 164 " --> pdb=" O PHE E 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 339 through 343 Processing helix chain 'H' and resid 23 through 61 Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.512A pdb=" N THR H 283 " --> pdb=" O HIS H 279 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU H 284 " --> pdb=" O SER H 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 279 through 284' Processing helix chain 'H' and resid 336 through 347 Processing helix chain 'H' and resid 438 through 453 Processing helix chain 'H' and resid 456 through 463 Processing helix chain 'H' and resid 467 through 482 removed outlier: 3.540A pdb=" N SER H 479 " --> pdb=" O ARG H 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 544 Processing helix chain 'H' and resid 576 through 581 Processing helix chain 'H' and resid 609 through 614 Processing helix chain 'H' and resid 652 through 665 Processing helix chain 'H' and resid 687 through 691 removed outlier: 3.582A pdb=" N PHE H 691 " --> pdb=" O LYS H 688 " (cutoff:3.500A) Processing helix chain 'H' and resid 730 through 734 Processing helix chain 'I' and resid 81 through 107 Proline residue: I 93 - end of helix Processing helix chain 'I' and resid 131 through 133 No H-bonds generated for 'chain 'I' and resid 131 through 133' Processing helix chain 'I' and resid 134 through 139 Processing helix chain 'I' and resid 459 through 462 Processing helix chain 'I' and resid 463 through 471 removed outlier: 3.991A pdb=" N LYS I 468 " --> pdb=" O LEU I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 502 through 506 Processing helix chain 'I' and resid 539 through 544 removed outlier: 3.865A pdb=" N PHE I 543 " --> pdb=" O SER I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 575 through 580 removed outlier: 4.048A pdb=" N GLU I 580 " --> pdb=" O GLN I 577 " (cutoff:3.500A) Processing helix chain 'I' and resid 589 through 602 Processing helix chain 'I' and resid 607 through 625 Processing helix chain 'I' and resid 628 through 651 removed outlier: 3.884A pdb=" N ASN I 633 " --> pdb=" O ASP I 629 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS I 634 " --> pdb=" O ASN I 630 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET I 637 " --> pdb=" O ASN I 633 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE I 639 " --> pdb=" O ALA I 635 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL I 640 " --> pdb=" O CYS I 636 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU I 641 " --> pdb=" O MET I 637 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN I 642 " --> pdb=" O LEU I 638 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY I 644 " --> pdb=" O VAL I 640 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN I 645 " --> pdb=" O GLU I 641 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LYS I 646 " --> pdb=" O ASN I 642 " (cutoff:3.500A) Processing helix chain 'I' and resid 652 through 662 Processing helix chain 'I' and resid 663 through 667 Processing helix chain 'I' and resid 670 through 689 removed outlier: 4.052A pdb=" N MET I 684 " --> pdb=" O LYS I 680 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 27 removed outlier: 3.910A pdb=" N LYS K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN K 27 " --> pdb=" O ILE K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 362 Processing helix chain 'M' and resid 193 through 210 removed outlier: 4.545A pdb=" N ALA M 197 " --> pdb=" O GLN M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 262 Processing helix chain 'M' and resid 273 through 281 removed outlier: 4.497A pdb=" N LEU M 278 " --> pdb=" O LYS M 274 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU M 279 " --> pdb=" O ASP M 275 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP M 281 " --> pdb=" O ALA M 277 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 292 removed outlier: 4.409A pdb=" N LYS M 291 " --> pdb=" O MET M 288 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG M 292 " --> pdb=" O PRO M 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 288 through 292' Processing helix chain 'L' and resid 142 through 148 removed outlier: 3.861A pdb=" N ASP L 146 " --> pdb=" O THR L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 164 removed outlier: 3.787A pdb=" N ARG L 164 " --> pdb=" O PHE L 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 279 removed outlier: 3.573A pdb=" N MET J 271 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 removed outlier: 3.501A pdb=" N GLN A 94 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100 removed outlier: 6.316A pdb=" N LYS A 99 " --> pdb=" O VAL C 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.200A pdb=" N SER A 114 " --> pdb=" O GLY A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 121 removed outlier: 6.270A pdb=" N PHE A 120 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 619 through 623 Processing sheet with id=AA6, first strand: chain 'A' and resid 642 through 645 removed outlier: 7.318A pdb=" N PHE A 642 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 717 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 644 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 185 through 188 Processing sheet with id=AA8, first strand: chain 'B' and resid 313 through 318 removed outlier: 3.703A pdb=" N LEU B 359 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B 315 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE B 357 " --> pdb=" O TYR B 315 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B 317 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 355 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 475 through 476 Processing sheet with id=AB1, first strand: chain 'B' and resid 557 through 560 removed outlier: 3.836A pdb=" N LEU B 529 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL D 35 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN D 403 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D 379 " --> pdb=" O VAL D 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 565 through 566 removed outlier: 4.013A pdb=" N TYR B 565 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 64 through 67 removed outlier: 6.929A pdb=" N ILE D 81 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 139 through 143 Processing sheet with id=AB5, first strand: chain 'D' and resid 193 through 196 Processing sheet with id=AB6, first strand: chain 'D' and resid 230 through 235 removed outlier: 3.870A pdb=" N ASP D 232 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 246 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 278 through 279 removed outlier: 3.565A pdb=" N CYS D 278 " --> pdb=" O GLY D 292 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 291 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA D 299 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 320 through 323 removed outlier: 3.700A pdb=" N LEU D 333 " --> pdb=" O TRP D 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 219 through 220 Processing sheet with id=AC1, first strand: chain 'F' and resid 224 through 226 Processing sheet with id=AC2, first strand: chain 'C' and resid 82 through 87 removed outlier: 7.336A pdb=" N ARG C 436 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 99 through 101 removed outlier: 3.894A pdb=" N GLN C 100 " --> pdb=" O ALA C 114 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 114 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 113 " --> pdb=" O TYR C 124 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 131 " --> pdb=" O HIS C 127 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 151 through 154 removed outlier: 6.024A pdb=" N ILE C 172 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS C 185 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE C 174 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 193 through 198 removed outlier: 3.986A pdb=" N GLU C 195 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 227 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN C 219 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 225 " --> pdb=" O ASN C 219 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N GLN C 292 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL C 226 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE C 294 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE C 228 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 242 through 244 removed outlier: 3.710A pdb=" N MET C 252 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 251 " --> pdb=" O TRP C 263 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 309 through 311 removed outlier: 3.780A pdb=" N SER C 323 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS C 332 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE C 352 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.854A pdb=" N ALA C 378 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR C 387 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 388 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR C 402 " --> pdb=" O VAL C 388 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 114 through 115 removed outlier: 5.829A pdb=" N SER H 114 " --> pdb=" O GLY H 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 619 through 623 Processing sheet with id=AD2, first strand: chain 'H' and resid 642 through 645 removed outlier: 7.182A pdb=" N PHE H 642 " --> pdb=" O ALA H 717 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA H 717 " --> pdb=" O PHE H 642 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER H 644 " --> pdb=" O ILE H 715 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET H 705 " --> pdb=" O ARG H 712 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 649 through 651 Processing sheet with id=AD4, first strand: chain 'I' and resid 185 through 188 removed outlier: 4.056A pdb=" N GLU I 185 " --> pdb=" O ARG I 253 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 313 through 318 removed outlier: 3.733A pdb=" N LEU I 359 " --> pdb=" O GLY I 313 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE I 357 " --> pdb=" O TYR I 315 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL I 317 " --> pdb=" O LEU I 355 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU I 355 " --> pdb=" O VAL I 317 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 429 through 433 removed outlier: 6.051A pdb=" N PHE I 429 " --> pdb=" O ILE I 487 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL I 489 " --> pdb=" O PHE I 429 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN I 431 " --> pdb=" O VAL I 489 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE I 491 " --> pdb=" O GLN I 431 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU I 433 " --> pdb=" O ILE I 491 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 557 through 560 removed outlier: 3.856A pdb=" N LEU I 529 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL K 35 " --> pdb=" O LEU I 529 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU K 34 " --> pdb=" O GLN K 403 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP K 379 " --> pdb=" O VAL K 393 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 565 through 566 removed outlier: 3.982A pdb=" N TYR I 565 " --> pdb=" O LEU I 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 64 through 67 removed outlier: 5.393A pdb=" N LEU K 79 " --> pdb=" O LYS K 120 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS K 120 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE K 81 " --> pdb=" O GLU K 118 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 139 through 143 Processing sheet with id=AE2, first strand: chain 'K' and resid 193 through 196 Processing sheet with id=AE3, first strand: chain 'K' and resid 230 through 235 removed outlier: 4.316A pdb=" N ASP K 232 " --> pdb=" O VAL K 246 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL K 246 " --> pdb=" O ASP K 232 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 322 through 325 Processing sheet with id=AE5, first strand: chain 'M' and resid 219 through 220 removed outlier: 3.529A pdb=" N VAL M 267 " --> pdb=" O VAL M 220 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 224 through 226 Processing sheet with id=AE7, first strand: chain 'J' and resid 82 through 87 removed outlier: 7.152A pdb=" N ARG J 436 " --> pdb=" O VAL J 85 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER J 87 " --> pdb=" O ILE J 434 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE J 434 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER J 417 " --> pdb=" O ILE J 426 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL J 428 " --> pdb=" O GLN J 415 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN J 415 " --> pdb=" O VAL J 428 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 100 through 101 removed outlier: 3.809A pdb=" N GLN J 100 " --> pdb=" O ALA J 114 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE J 113 " --> pdb=" O TYR J 124 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR J 124 " --> pdb=" O PHE J 113 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN J 136 " --> pdb=" O LEU J 123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 149 through 155 removed outlier: 3.762A pdb=" N ALA J 166 " --> pdb=" O THR J 149 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS J 160 " --> pdb=" O ASP J 155 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN J 181 " --> pdb=" O ASN J 176 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 193 through 198 removed outlier: 4.098A pdb=" N GLU J 195 " --> pdb=" O VAL J 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL J 209 " --> pdb=" O GLU J 195 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU J 215 " --> pdb=" O ILE J 228 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE J 228 " --> pdb=" O LEU J 215 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU J 217 " --> pdb=" O VAL J 226 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN J 292 " --> pdb=" O VAL J 226 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 239 through 242 removed outlier: 3.650A pdb=" N SER J 241 " --> pdb=" O CYS J 254 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 309 through 311 removed outlier: 3.546A pdb=" N TRP J 331 " --> pdb=" O ILE J 319 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER J 321 " --> pdb=" O VAL J 329 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER J 323 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA J 327 " --> pdb=" O SER J 323 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE J 356 " --> pdb=" O ILE J 328 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY J 354 " --> pdb=" O CYS J 330 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS J 332 " --> pdb=" O ILE J 352 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE J 352 " --> pdb=" O LYS J 332 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 368 through 370 removed outlier: 3.586A pdb=" N LEU J 379 " --> pdb=" O TYR J 387 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR J 387 " --> pdb=" O LEU J 379 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR J 402 " --> pdb=" O VAL J 388 " (cutoff:3.500A) 742 hydrogen bonds defined for protein. 2037 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.01 Time building geometry restraints manager: 7.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8305 1.34 - 1.46: 6201 1.46 - 1.59: 10383 1.59 - 1.71: 18 1.71 - 1.83: 134 Bond restraints: 25041 Sorted by residual: bond pdb=" CA CYS H 576 " pdb=" C CYS H 576 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N ASN H 572 " pdb=" CA ASN H 572 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.33e-02 5.65e+03 7.68e+00 bond pdb=" N ARG A 566 " pdb=" CA ARG A 566 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.66e+00 bond pdb=" N ASN A 572 " pdb=" CA ASN A 572 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.33e-02 5.65e+03 6.61e+00 bond pdb=" N LYS H 574 " pdb=" CA LYS H 574 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.35e-02 5.49e+03 4.73e+00 ... (remaining 25036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 34341 4.14 - 8.28: 47 8.28 - 12.41: 3 12.41 - 16.55: 1 16.55 - 20.69: 1 Bond angle restraints: 34393 Sorted by residual: angle pdb=" C GLN A 575 " pdb=" CA GLN A 575 " pdb=" CB GLN A 575 " ideal model delta sigma weight residual 110.96 90.27 20.69 1.54e+00 4.22e-01 1.80e+02 angle pdb=" N ARG A 566 " pdb=" CA ARG A 566 " pdb=" C ARG A 566 " ideal model delta sigma weight residual 112.26 103.19 9.07 1.32e+00 5.74e-01 4.72e+01 angle pdb=" C ALA E 141 " pdb=" CA ALA E 141 " pdb=" CB ALA E 141 " ideal model delta sigma weight residual 116.54 110.02 6.52 1.15e+00 7.56e-01 3.22e+01 angle pdb=" C CYS H 576 " pdb=" N PRO H 577 " pdb=" CA PRO H 577 " ideal model delta sigma weight residual 119.84 126.69 -6.85 1.25e+00 6.40e-01 3.01e+01 angle pdb=" C CYS H 576 " pdb=" CA CYS H 576 " pdb=" CB CYS H 576 " ideal model delta sigma weight residual 109.82 118.83 -9.01 1.65e+00 3.67e-01 2.98e+01 ... (remaining 34388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13330 17.93 - 35.85: 944 35.85 - 53.78: 282 53.78 - 71.70: 59 71.70 - 89.63: 10 Dihedral angle restraints: 14625 sinusoidal: 4123 harmonic: 10502 Sorted by residual: dihedral pdb=" C GLN A 575 " pdb=" N GLN A 575 " pdb=" CA GLN A 575 " pdb=" CB GLN A 575 " ideal model delta harmonic sigma weight residual -122.60 -100.39 -22.21 0 2.50e+00 1.60e-01 7.89e+01 dihedral pdb=" CB CYS A 325 " pdb=" SG CYS A 325 " pdb=" SG CYS A 457 " pdb=" CB CYS A 457 " ideal model delta sinusoidal sigma weight residual 93.00 142.83 -49.83 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" C CYS H 576 " pdb=" N CYS H 576 " pdb=" CA CYS H 576 " pdb=" CB CYS H 576 " ideal model delta harmonic sigma weight residual -122.60 -133.71 11.11 0 2.50e+00 1.60e-01 1.98e+01 ... (remaining 14622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3499 0.069 - 0.139: 422 0.139 - 0.208: 6 0.208 - 0.277: 1 0.277 - 0.347: 1 Chirality restraints: 3929 Sorted by residual: chirality pdb=" CA GLN A 575 " pdb=" N GLN A 575 " pdb=" C GLN A 575 " pdb=" CB GLN A 575 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA CYS H 576 " pdb=" N CYS H 576 " pdb=" C CYS H 576 " pdb=" CB CYS H 576 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB THR A 344 " pdb=" CA THR A 344 " pdb=" OG1 THR A 344 " pdb=" CG2 THR A 344 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.57e-01 ... (remaining 3926 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 566 " -0.483 9.50e-02 1.11e+02 2.17e-01 2.87e+01 pdb=" NE ARG H 566 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG H 566 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 566 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 566 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 566 " 0.330 9.50e-02 1.11e+02 1.48e-01 1.37e+01 pdb=" NE ARG A 566 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 566 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 566 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 566 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 99 " 0.018 2.00e-02 2.50e+03 2.39e-02 9.96e+00 pdb=" CG PHE I 99 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE I 99 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE I 99 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE I 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 99 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE I 99 " -0.008 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2479 2.75 - 3.28: 24053 3.28 - 3.82: 40251 3.82 - 4.36: 42425 4.36 - 4.90: 75306 Nonbonded interactions: 184514 Sorted by model distance: nonbonded pdb=" OG1 THR I 523 " pdb=" O HIS I 561 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR K 46 " pdb=" O ASN K 128 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS C 332 " pdb=" O LYS C 335 " model vdw 2.211 3.120 nonbonded pdb=" O TRP K 49 " pdb=" OH TYR K 132 " model vdw 2.211 3.040 nonbonded pdb=" O SER I 662 " pdb=" OG SER I 662 " model vdw 2.217 3.040 ... (remaining 184509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'H' and (resid 22 through 330 or (resid 331 and (name N or name CA or nam \ e C or name O or name CB )) or resid 332 through 737 or resid 801 through 807)) } ncs_group { reference = chain 'B' selection = (chain 'I' and (resid 80 through 138 or (resid 139 through 162 and (name N or na \ me CA or name C or name O or name CB )) or resid 163 through 689)) } ncs_group { reference = (chain 'C' and (resid 77 through 208 or (resid 209 through 210 and (name N or na \ me CA or name C or name O or name CB )) or resid 211 through 441)) selection = chain 'J' } ncs_group { reference = chain 'D' selection = (chain 'K' and (resid 3 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB )) or resid 205 through 411)) } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 60.280 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25099 Z= 0.134 Angle : 0.685 54.611 34469 Z= 0.324 Chirality : 0.042 0.347 3929 Planarity : 0.005 0.217 4537 Dihedral : 14.772 89.628 7743 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.17 % Favored : 91.66 % Rotamer: Outliers : 2.18 % Allowed : 26.22 % Favored : 71.60 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3502 helix: 1.70 (0.21), residues: 666 sheet: -1.46 (0.21), residues: 634 loop : -1.46 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 314 HIS 0.010 0.001 HIS A 694 PHE 0.054 0.001 PHE I 99 TYR 0.015 0.001 TYR I 643 ARG 0.009 0.000 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.23206 ( 742) hydrogen bonds : angle 8.17538 ( 2037) metal coordination : bond 0.00843 ( 56) metal coordination : angle 8.75424 ( 72) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.75418 ( 4) covalent geometry : bond 0.00242 (25041) covalent geometry : angle 0.55621 (34393) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 315 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.5937 (ppp) cc_final: 0.5689 (ppp) REVERT: A 285 PHE cc_start: 0.3738 (p90) cc_final: 0.3453 (p90) outliers start: 39 outliers final: 18 residues processed: 345 average time/residue: 0.3692 time to fit residues: 200.9451 Evaluate side-chains 243 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain K residue 277 ASN Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain J residue 356 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 8.9990 chunk 269 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 278 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 322 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS D 78 HIS ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 527 HIS I 620 HIS I 655 ASN K 277 ASN K 343 ASN J 92 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.127343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.109718 restraints weight = 124960.761| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 5.46 r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4342 r_free = 0.4342 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4343 r_free = 0.4343 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 25099 Z= 0.186 Angle : 0.704 34.201 34469 Z= 0.336 Chirality : 0.044 0.197 3929 Planarity : 0.004 0.047 4537 Dihedral : 6.775 63.823 3914 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.77 % Favored : 90.09 % Rotamer: Outliers : 5.04 % Allowed : 22.75 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3502 helix: 1.26 (0.20), residues: 678 sheet: -1.47 (0.21), residues: 622 loop : -1.66 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 402 HIS 0.007 0.001 HIS D 311 PHE 0.036 0.002 PHE A 474 TYR 0.026 0.002 TYR H 731 ARG 0.009 0.001 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 742) hydrogen bonds : angle 6.39055 ( 2037) metal coordination : bond 0.01734 ( 56) metal coordination : angle 7.56022 ( 72) SS BOND : bond 0.00212 ( 2) SS BOND : angle 3.70561 ( 4) covalent geometry : bond 0.00401 (25041) covalent geometry : angle 0.61301 (34393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 248 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 TRP cc_start: 0.0781 (OUTLIER) cc_final: -0.0297 (m-90) REVERT: A 651 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7336 (pt) REVERT: A 729 PHE cc_start: 0.6984 (m-80) cc_final: 0.5911 (m-10) REVERT: B 113 ARG cc_start: 0.2594 (ttm170) cc_final: -0.1191 (tpt-90) REVERT: B 579 MET cc_start: 0.4820 (mtp) cc_final: 0.4221 (ptp) REVERT: C 252 MET cc_start: 0.6264 (tpt) cc_final: 0.6025 (tpt) REVERT: C 253 SER cc_start: 0.6844 (OUTLIER) cc_final: 0.6598 (m) REVERT: C 271 MET cc_start: 0.8084 (ppp) cc_final: 0.7782 (ppp) REVERT: C 332 LYS cc_start: 0.7936 (tptt) cc_final: 0.7677 (tptt) REVERT: C 358 TYR cc_start: 0.0275 (OUTLIER) cc_final: -0.0483 (p90) REVERT: C 369 SER cc_start: 0.6856 (m) cc_final: 0.6281 (p) REVERT: H 333 LEU cc_start: 0.3873 (mt) cc_final: 0.3436 (mm) REVERT: I 117 TYR cc_start: 0.3757 (OUTLIER) cc_final: 0.1152 (t80) REVERT: I 661 VAL cc_start: 0.8812 (t) cc_final: 0.8527 (p) REVERT: J 414 ARG cc_start: 0.8346 (mmp-170) cc_final: 0.6711 (tmt-80) outliers start: 90 outliers final: 48 residues processed: 317 average time/residue: 0.3308 time to fit residues: 169.5079 Evaluate side-chains 269 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain H residue 582 VAL Chi-restraints excluded: chain H residue 611 ILE Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 598 THR Chi-restraints excluded: chain I residue 600 ILE Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 277 ASN Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 375 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 296 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 322 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 140 optimal weight: 0.0050 chunk 20 optimal weight: 0.2980 chunk 319 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 333 optimal weight: 0.9980 chunk 342 optimal weight: 4.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 ASN H 118 GLN ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.131971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.113772 restraints weight = 119063.317| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 5.36 r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4437 r_free = 0.4437 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4437 r_free = 0.4437 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25099 Z= 0.103 Angle : 0.577 27.967 34469 Z= 0.274 Chirality : 0.042 0.167 3929 Planarity : 0.003 0.037 4537 Dihedral : 6.357 63.802 3906 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.51 % Favored : 92.38 % Rotamer: Outliers : 3.42 % Allowed : 24.09 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3502 helix: 1.67 (0.20), residues: 682 sheet: -1.38 (0.20), residues: 648 loop : -1.55 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 345 HIS 0.007 0.001 HIS K 239 PHE 0.032 0.001 PHE I 86 TYR 0.010 0.001 TYR I 117 ARG 0.007 0.000 ARG J 306 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 742) hydrogen bonds : angle 5.66865 ( 2037) metal coordination : bond 0.00788 ( 56) metal coordination : angle 5.66197 ( 72) SS BOND : bond 0.00442 ( 2) SS BOND : angle 3.66055 ( 4) covalent geometry : bond 0.00215 (25041) covalent geometry : angle 0.51458 (34393) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6044 (ppp) cc_final: 0.5802 (ppp) REVERT: A 729 PHE cc_start: 0.7069 (m-80) cc_final: 0.5987 (m-10) REVERT: B 113 ARG cc_start: 0.2272 (ttm170) cc_final: -0.0999 (tpt-90) REVERT: D 25 LYS cc_start: 0.5964 (mttt) cc_final: 0.5741 (mttm) REVERT: D 117 ILE cc_start: 0.6408 (mm) cc_final: 0.6130 (mm) REVERT: C 358 TYR cc_start: 0.0754 (OUTLIER) cc_final: 0.0085 (p90) REVERT: H 110 MET cc_start: 0.7096 (ppp) cc_final: 0.6749 (ppp) REVERT: H 333 LEU cc_start: 0.3703 (mt) cc_final: 0.3298 (mm) REVERT: I 117 TYR cc_start: 0.2793 (OUTLIER) cc_final: 0.0205 (t80) REVERT: I 661 VAL cc_start: 0.8747 (t) cc_final: 0.8477 (p) REVERT: K 195 SER cc_start: 0.6355 (OUTLIER) cc_final: 0.5874 (p) REVERT: M 268 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.6852 (t70) outliers start: 61 outliers final: 35 residues processed: 288 average time/residue: 0.3351 time to fit residues: 156.9695 Evaluate side-chains 256 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 621 LEU Chi-restraints excluded: chain H residue 726 GLU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 388 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 146 optimal weight: 8.9990 chunk 269 optimal weight: 6.9990 chunk 302 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 135 optimal weight: 0.2980 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS A 618 HIS A 676 ASN D 27 ASN D 64 HIS ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 685 GLN ** K 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 326 ASN J 381 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.122267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.104847 restraints weight = 125585.482| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 5.65 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4254 r_free = 0.4254 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4256 r_free = 0.4256 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.4256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 25099 Z= 0.235 Angle : 0.767 46.822 34469 Z= 0.368 Chirality : 0.045 0.172 3929 Planarity : 0.005 0.054 4537 Dihedral : 6.973 63.852 3902 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.79 % Favored : 89.03 % Rotamer: Outliers : 6.39 % Allowed : 22.63 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.14), residues: 3502 helix: 0.97 (0.20), residues: 674 sheet: -1.49 (0.20), residues: 698 loop : -1.83 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D 402 HIS 0.008 0.002 HIS D 316 PHE 0.031 0.003 PHE D 108 TYR 0.026 0.003 TYR I 117 ARG 0.006 0.001 ARG J 436 Details of bonding type rmsd hydrogen bonds : bond 0.05157 ( 742) hydrogen bonds : angle 6.36599 ( 2037) metal coordination : bond 0.02000 ( 56) metal coordination : angle 7.98941 ( 72) SS BOND : bond 0.00149 ( 2) SS BOND : angle 2.05179 ( 4) covalent geometry : bond 0.00518 (25041) covalent geometry : angle 0.67535 (34393) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 224 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 TRP cc_start: 0.1364 (OUTLIER) cc_final: -0.0096 (m-90) REVERT: A 729 PHE cc_start: 0.7291 (m-80) cc_final: 0.6131 (m-10) REVERT: B 113 ARG cc_start: 0.3112 (ttm170) cc_final: -0.0047 (ttt90) REVERT: B 514 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7425 (p90) REVERT: B 663 MET cc_start: 0.6650 (ppp) cc_final: 0.6393 (ppp) REVERT: C 332 LYS cc_start: 0.8251 (tptt) cc_final: 0.7865 (tptt) REVERT: C 358 TYR cc_start: 0.0467 (OUTLIER) cc_final: -0.0515 (p90) REVERT: H 333 LEU cc_start: 0.4217 (mt) cc_final: 0.3881 (mm) REVERT: H 615 SER cc_start: 0.5111 (OUTLIER) cc_final: 0.4664 (m) REVERT: I 117 TYR cc_start: 0.3384 (OUTLIER) cc_final: 0.1056 (t80) REVERT: I 595 LYS cc_start: 0.3395 (OUTLIER) cc_final: 0.3047 (tttt) REVERT: K 409 TYR cc_start: 0.6044 (OUTLIER) cc_final: 0.5552 (t80) REVERT: J 136 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7021 (mt0) outliers start: 114 outliers final: 58 residues processed: 325 average time/residue: 0.3284 time to fit residues: 173.3126 Evaluate side-chains 284 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 218 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 514 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain H residue 731 TYR Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 449 HIS Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 595 LYS Chi-restraints excluded: chain I residue 666 PHE Chi-restraints excluded: chain I residue 688 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 356 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 47 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 353 optimal weight: 8.9990 chunk 283 optimal weight: 30.0000 chunk 299 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 HIS C 219 ASN ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS ** K 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.118995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.101676 restraints weight = 119597.530| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 5.26 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4205 r_free = 0.4205 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4205 r_free = 0.4205 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.4205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 25099 Z= 0.304 Angle : 0.889 57.179 34469 Z= 0.426 Chirality : 0.048 0.212 3929 Planarity : 0.006 0.070 4537 Dihedral : 7.528 63.917 3898 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.08 % Favored : 87.69 % Rotamer: Outliers : 7.17 % Allowed : 23.14 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.14), residues: 3502 helix: 0.37 (0.20), residues: 638 sheet: -1.74 (0.20), residues: 648 loop : -2.29 (0.12), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP K 382 HIS 0.016 0.002 HIS B 449 PHE 0.032 0.003 PHE D 368 TYR 0.031 0.003 TYR B 643 ARG 0.014 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.05938 ( 742) hydrogen bonds : angle 7.04820 ( 2037) metal coordination : bond 0.02197 ( 56) metal coordination : angle 9.55605 ( 72) SS BOND : bond 0.01267 ( 2) SS BOND : angle 1.58470 ( 4) covalent geometry : bond 0.00661 (25041) covalent geometry : angle 0.77464 (34393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 221 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 TRP cc_start: 0.2121 (OUTLIER) cc_final: -0.0565 (m-90) REVERT: A 729 PHE cc_start: 0.7603 (m-80) cc_final: 0.6998 (m-80) REVERT: B 455 LEU cc_start: 0.0331 (mt) cc_final: 0.0129 (mt) REVERT: B 514 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7338 (p90) REVERT: C 101 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.5070 (t80) REVERT: C 127 HIS cc_start: 0.6216 (OUTLIER) cc_final: 0.5750 (m170) REVERT: C 219 ASN cc_start: 0.7413 (t0) cc_final: 0.6998 (t0) REVERT: C 244 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: C 271 MET cc_start: 0.8040 (ppp) cc_final: 0.7610 (ppp) REVERT: C 332 LYS cc_start: 0.7927 (tptt) cc_final: 0.7353 (tptt) REVERT: C 358 TYR cc_start: 0.1796 (OUTLIER) cc_final: 0.0847 (p90) REVERT: H 270 LYS cc_start: 0.7178 (ptmt) cc_final: 0.6105 (mptt) REVERT: H 333 LEU cc_start: 0.4914 (mt) cc_final: 0.4640 (mm) REVERT: H 437 TRP cc_start: 0.1231 (OUTLIER) cc_final: 0.0823 (t-100) REVERT: I 527 HIS cc_start: 0.4771 (OUTLIER) cc_final: 0.4445 (m90) REVERT: I 661 VAL cc_start: 0.8857 (t) cc_final: 0.8597 (p) REVERT: K 409 TYR cc_start: 0.5901 (OUTLIER) cc_final: 0.5537 (t80) REVERT: M 281 ASP cc_start: 0.2179 (OUTLIER) cc_final: 0.1687 (t70) REVERT: J 136 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6983 (mt0) REVERT: J 336 MET cc_start: 0.7867 (mtp) cc_final: 0.6831 (tpp) REVERT: J 366 MET cc_start: 0.7538 (ptm) cc_final: 0.7294 (ptp) REVERT: J 377 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7555 (tt) outliers start: 128 outliers final: 77 residues processed: 323 average time/residue: 0.3197 time to fit residues: 173.5947 Evaluate side-chains 296 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 207 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 83 HIS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 514 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 127 HIS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain H residue 41 MET Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain H residue 582 VAL Chi-restraints excluded: chain H residue 611 ILE Chi-restraints excluded: chain H residue 729 PHE Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 449 HIS Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 527 HIS Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 598 THR Chi-restraints excluded: chain I residue 600 ILE Chi-restraints excluded: chain I residue 630 ASN Chi-restraints excluded: chain I residue 656 PHE Chi-restraints excluded: chain I residue 666 PHE Chi-restraints excluded: chain I residue 667 ASN Chi-restraints excluded: chain I residue 688 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 281 ASP Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 308 TYR Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 353 LEU Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 377 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 74 optimal weight: 7.9990 chunk 330 optimal weight: 0.9980 chunk 306 optimal weight: 2.9990 chunk 53 optimal weight: 50.0000 chunk 335 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 348 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 204 optimal weight: 0.0060 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN H 118 GLN ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 370 HIS M 200 HIS ** J 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.123455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.106780 restraints weight = 121421.645| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 5.19 r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25099 Z= 0.123 Angle : 0.645 34.385 34469 Z= 0.306 Chirality : 0.043 0.159 3929 Planarity : 0.004 0.048 4537 Dihedral : 6.796 63.838 3898 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.99 % Favored : 90.81 % Rotamer: Outliers : 3.92 % Allowed : 26.39 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3502 helix: 0.81 (0.20), residues: 688 sheet: -1.55 (0.21), residues: 616 loop : -2.08 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 599 HIS 0.030 0.001 HIS K 192 PHE 0.022 0.001 PHE C 299 TYR 0.020 0.001 TYR B 643 ARG 0.006 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 742) hydrogen bonds : angle 6.09226 ( 2037) metal coordination : bond 0.01185 ( 56) metal coordination : angle 6.50140 ( 72) SS BOND : bond 0.00603 ( 2) SS BOND : angle 0.89246 ( 4) covalent geometry : bond 0.00260 (25041) covalent geometry : angle 0.57316 (34393) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 227 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.5498 (mmp-170) cc_final: 0.4964 (mmp80) REVERT: A 110 MET cc_start: 0.5988 (ppp) cc_final: 0.5758 (ppp) REVERT: A 437 TRP cc_start: 0.1889 (OUTLIER) cc_final: 0.0480 (m-90) REVERT: A 457 CYS cc_start: 0.3709 (OUTLIER) cc_final: 0.3349 (p) REVERT: A 729 PHE cc_start: 0.7433 (m-80) cc_final: 0.6852 (m-10) REVERT: B 113 ARG cc_start: 0.3224 (ttm170) cc_final: 0.0576 (tpt-90) REVERT: B 514 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7172 (p90) REVERT: B 663 MET cc_start: 0.6265 (ppp) cc_final: 0.5838 (ppp) REVERT: B 680 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6971 (mmtm) REVERT: D 312 SER cc_start: 0.9029 (m) cc_final: 0.8737 (t) REVERT: C 219 ASN cc_start: 0.7172 (t0) cc_final: 0.6759 (t0) REVERT: C 271 MET cc_start: 0.7834 (ppp) cc_final: 0.7519 (ppp) REVERT: C 358 TYR cc_start: 0.1913 (OUTLIER) cc_final: 0.1179 (p90) REVERT: I 468 LYS cc_start: 0.8435 (mttt) cc_final: 0.8196 (mptt) REVERT: I 643 TYR cc_start: 0.5788 (m-80) cc_final: 0.5408 (m-80) REVERT: I 661 VAL cc_start: 0.8796 (t) cc_final: 0.8545 (p) REVERT: K 66 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5410 (tp) REVERT: K 409 TYR cc_start: 0.5751 (OUTLIER) cc_final: 0.5437 (t80) REVERT: M 268 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.6513 (t70) REVERT: J 136 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6953 (mt0) REVERT: J 336 MET cc_start: 0.7740 (mtp) cc_final: 0.7065 (tpp) REVERT: J 377 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6399 (tt) outliers start: 70 outliers final: 43 residues processed: 281 average time/residue: 0.3241 time to fit residues: 150.4659 Evaluate side-chains 272 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 83 HIS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 514 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 680 LYS Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain H residue 621 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 656 PHE Chi-restraints excluded: chain I residue 688 LEU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 345 TRP Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 377 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 222 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 198 optimal weight: 6.9990 chunk 162 optimal weight: 0.0270 chunk 163 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 527 HIS ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS ** K 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.122194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.105357 restraints weight = 120447.122| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 5.20 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25099 Z= 0.149 Angle : 0.652 36.381 34469 Z= 0.309 Chirality : 0.043 0.163 3929 Planarity : 0.004 0.049 4537 Dihedral : 6.748 63.839 3898 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.94 % Favored : 89.86 % Rotamer: Outliers : 4.26 % Allowed : 26.44 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.14), residues: 3502 helix: 1.00 (0.20), residues: 674 sheet: -1.58 (0.20), residues: 646 loop : -2.05 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 599 HIS 0.008 0.001 HIS C 199 PHE 0.023 0.002 PHE A 285 TYR 0.020 0.002 TYR B 495 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 742) hydrogen bonds : angle 5.97222 ( 2037) metal coordination : bond 0.01479 ( 56) metal coordination : angle 6.58771 ( 72) SS BOND : bond 0.00608 ( 2) SS BOND : angle 0.77933 ( 4) covalent geometry : bond 0.00327 (25041) covalent geometry : angle 0.57876 (34393) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 216 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.5513 (mmp-170) cc_final: 0.5101 (mmp80) REVERT: A 437 TRP cc_start: 0.1987 (OUTLIER) cc_final: 0.0579 (m-90) REVERT: A 457 CYS cc_start: 0.3696 (OUTLIER) cc_final: 0.3230 (p) REVERT: A 729 PHE cc_start: 0.7414 (m-80) cc_final: 0.7109 (m-80) REVERT: B 113 ARG cc_start: 0.3306 (ttm170) cc_final: 0.0648 (tpt-90) REVERT: B 514 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7267 (p90) REVERT: B 572 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7353 (mm) REVERT: C 332 LYS cc_start: 0.7832 (tptt) cc_final: 0.7344 (tptt) REVERT: C 358 TYR cc_start: 0.1631 (OUTLIER) cc_final: 0.0915 (p90) REVERT: H 110 MET cc_start: 0.7266 (ppp) cc_final: 0.7023 (ppp) REVERT: H 270 LYS cc_start: 0.7090 (ptmt) cc_final: 0.5879 (mptt) REVERT: H 437 TRP cc_start: 0.1483 (OUTLIER) cc_final: 0.1210 (m-90) REVERT: H 545 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8525 (tp40) REVERT: I 595 LYS cc_start: 0.3762 (OUTLIER) cc_final: 0.3250 (tttt) REVERT: I 661 VAL cc_start: 0.8928 (t) cc_final: 0.8650 (p) REVERT: K 66 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5453 (tp) REVERT: K 409 TYR cc_start: 0.5598 (OUTLIER) cc_final: 0.5305 (t80) REVERT: J 136 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6797 (mt0) REVERT: J 336 MET cc_start: 0.7734 (mtp) cc_final: 0.7085 (tpp) REVERT: J 377 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7078 (tt) REVERT: J 438 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.6958 (m-30) outliers start: 76 outliers final: 52 residues processed: 276 average time/residue: 0.3300 time to fit residues: 150.6928 Evaluate side-chains 277 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 213 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 514 PHE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain H residue 621 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 595 LYS Chi-restraints excluded: chain I residue 656 PHE Chi-restraints excluded: chain I residue 663 MET Chi-restraints excluded: chain I residue 688 LEU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 345 TRP Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain J residue 438 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 181 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 66 optimal weight: 0.0870 chunk 80 optimal weight: 3.9990 chunk 307 optimal weight: 0.1980 chunk 338 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 330 optimal weight: 9.9990 chunk 235 optimal weight: 50.0000 chunk 347 optimal weight: 0.8980 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS D 272 HIS ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 38 HIS ** J 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.123840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.106848 restraints weight = 126657.655| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 5.18 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25099 Z= 0.109 Angle : 0.596 26.279 34469 Z= 0.285 Chirality : 0.042 0.163 3929 Planarity : 0.004 0.042 4537 Dihedral : 6.495 63.817 3898 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.60 % Favored : 91.26 % Rotamer: Outliers : 3.59 % Allowed : 27.11 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3502 helix: 1.28 (0.20), residues: 674 sheet: -1.36 (0.21), residues: 630 loop : -1.94 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 599 HIS 0.009 0.001 HIS C 199 PHE 0.017 0.001 PHE C 299 TYR 0.017 0.001 TYR I 643 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 742) hydrogen bonds : angle 5.55593 ( 2037) metal coordination : bond 0.01027 ( 56) metal coordination : angle 5.47935 ( 72) SS BOND : bond 0.00531 ( 2) SS BOND : angle 0.86460 ( 4) covalent geometry : bond 0.00238 (25041) covalent geometry : angle 0.54176 (34393) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 CYS cc_start: 0.7556 (t) cc_final: 0.7172 (t) REVERT: A 110 MET cc_start: 0.5992 (ppp) cc_final: 0.5757 (ppp) REVERT: A 121 MET cc_start: 0.8186 (tmm) cc_final: 0.7877 (tmm) REVERT: A 123 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6728 (tt0) REVERT: A 437 TRP cc_start: 0.1736 (OUTLIER) cc_final: 0.0433 (m-90) REVERT: A 457 CYS cc_start: 0.3605 (OUTLIER) cc_final: 0.3113 (p) REVERT: A 550 LYS cc_start: 0.6359 (OUTLIER) cc_final: 0.5499 (pttm) REVERT: B 113 ARG cc_start: 0.3102 (ttm170) cc_final: 0.0691 (tpt-90) REVERT: B 467 LEU cc_start: 0.5901 (tp) cc_final: 0.5229 (pp) REVERT: B 572 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7356 (mm) REVERT: C 332 LYS cc_start: 0.7982 (tptt) cc_final: 0.7493 (tptt) REVERT: C 358 TYR cc_start: 0.1310 (OUTLIER) cc_final: 0.0672 (p90) REVERT: H 110 MET cc_start: 0.7326 (ppp) cc_final: 0.7070 (ppp) REVERT: H 270 LYS cc_start: 0.7046 (ptmt) cc_final: 0.5843 (mptt) REVERT: H 545 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8439 (tp40) REVERT: I 117 TYR cc_start: 0.2143 (OUTLIER) cc_final: 0.0192 (t80) REVERT: I 595 LYS cc_start: 0.3677 (OUTLIER) cc_final: 0.3100 (tttt) REVERT: I 661 VAL cc_start: 0.8865 (t) cc_final: 0.8594 (p) REVERT: K 409 TYR cc_start: 0.5708 (OUTLIER) cc_final: 0.5422 (t80) REVERT: M 268 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.6842 (t70) REVERT: J 252 MET cc_start: 0.6694 (tpp) cc_final: 0.6385 (tpp) REVERT: J 336 MET cc_start: 0.7823 (mtp) cc_final: 0.7083 (tpp) REVERT: J 438 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.6733 (m-30) outliers start: 64 outliers final: 40 residues processed: 272 average time/residue: 0.3227 time to fit residues: 146.2205 Evaluate side-chains 263 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 621 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 595 LYS Chi-restraints excluded: chain I residue 663 MET Chi-restraints excluded: chain I residue 688 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 345 TRP Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain J residue 438 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 120 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 305 optimal weight: 0.9980 chunk 196 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 109 optimal weight: 30.0000 chunk 148 optimal weight: 5.9990 chunk 297 optimal weight: 8.9990 chunk 248 optimal weight: 0.0870 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS D 272 HIS ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.122396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.105303 restraints weight = 125813.627| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 5.18 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25099 Z= 0.139 Angle : 0.626 30.212 34469 Z= 0.300 Chirality : 0.043 0.200 3929 Planarity : 0.004 0.047 4537 Dihedral : 6.549 63.825 3897 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.51 % Favored : 90.35 % Rotamer: Outliers : 3.75 % Allowed : 27.06 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3502 helix: 1.31 (0.20), residues: 674 sheet: -1.44 (0.20), residues: 664 loop : -1.90 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 345 HIS 0.008 0.001 HIS C 199 PHE 0.025 0.002 PHE A 285 TYR 0.019 0.002 TYR B 495 ARG 0.003 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 742) hydrogen bonds : angle 5.57083 ( 2037) metal coordination : bond 0.01313 ( 56) metal coordination : angle 5.84110 ( 72) SS BOND : bond 0.00527 ( 2) SS BOND : angle 0.77809 ( 4) covalent geometry : bond 0.00305 (25041) covalent geometry : angle 0.56684 (34393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.5418 (mmp-170) cc_final: 0.4962 (mmp80) REVERT: A 83 CYS cc_start: 0.7689 (t) cc_final: 0.7343 (t) REVERT: A 437 TRP cc_start: 0.1863 (OUTLIER) cc_final: 0.0381 (m-90) REVERT: A 457 CYS cc_start: 0.3674 (OUTLIER) cc_final: 0.3132 (p) REVERT: B 113 ARG cc_start: 0.3253 (ttm170) cc_final: 0.0972 (tpt-90) REVERT: B 467 LEU cc_start: 0.5905 (tp) cc_final: 0.5201 (pp) REVERT: B 514 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7498 (p90) REVERT: B 572 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7257 (mm) REVERT: D 312 SER cc_start: 0.9117 (m) cc_final: 0.8827 (t) REVERT: C 332 LYS cc_start: 0.8071 (tptt) cc_final: 0.7560 (tptt) REVERT: C 358 TYR cc_start: 0.1348 (OUTLIER) cc_final: 0.0709 (p90) REVERT: H 110 MET cc_start: 0.7373 (ppp) cc_final: 0.7033 (ppp) REVERT: H 270 LYS cc_start: 0.7032 (ptmt) cc_final: 0.5842 (mptt) REVERT: I 117 TYR cc_start: 0.2327 (OUTLIER) cc_final: 0.0241 (t80) REVERT: I 595 LYS cc_start: 0.3827 (OUTLIER) cc_final: 0.3298 (tttt) REVERT: I 661 VAL cc_start: 0.8882 (t) cc_final: 0.8602 (p) REVERT: K 409 TYR cc_start: 0.5573 (OUTLIER) cc_final: 0.5263 (t80) REVERT: J 136 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6759 (mt0) REVERT: J 252 MET cc_start: 0.6619 (tpp) cc_final: 0.6409 (tpp) REVERT: J 336 MET cc_start: 0.7804 (mtp) cc_final: 0.7060 (tpp) outliers start: 67 outliers final: 47 residues processed: 267 average time/residue: 0.3355 time to fit residues: 147.1908 Evaluate side-chains 267 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 211 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 514 PHE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 576 CYS Chi-restraints excluded: chain H residue 621 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 595 LYS Chi-restraints excluded: chain I residue 663 MET Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 345 TRP Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 364 TRP Chi-restraints excluded: chain J residue 366 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 3 optimal weight: 9.9990 chunk 216 optimal weight: 0.0030 chunk 209 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 342 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 7 optimal weight: 30.0000 chunk 69 optimal weight: 9.9990 chunk 139 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 overall best weight: 2.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS B 481 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS D 343 ASN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.121773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.104902 restraints weight = 119662.561| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 5.31 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25099 Z= 0.153 Angle : 0.657 33.291 34469 Z= 0.313 Chirality : 0.043 0.215 3929 Planarity : 0.004 0.047 4537 Dihedral : 6.637 63.831 3897 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.99 % Favored : 89.83 % Rotamer: Outliers : 3.19 % Allowed : 27.68 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3502 helix: 1.23 (0.20), residues: 662 sheet: -1.41 (0.21), residues: 644 loop : -1.95 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP D 345 HIS 0.009 0.001 HIS C 199 PHE 0.016 0.002 PHE C 299 TYR 0.019 0.002 TYR B 495 ARG 0.004 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 742) hydrogen bonds : angle 5.72017 ( 2037) metal coordination : bond 0.01430 ( 56) metal coordination : angle 6.22347 ( 72) SS BOND : bond 0.00535 ( 2) SS BOND : angle 0.82219 ( 4) covalent geometry : bond 0.00338 (25041) covalent geometry : angle 0.59277 (34393) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.5356 (mmp-170) cc_final: 0.4823 (mmp80) REVERT: A 121 MET cc_start: 0.8372 (tmm) cc_final: 0.7754 (tmm) REVERT: A 437 TRP cc_start: 0.2011 (OUTLIER) cc_final: 0.0425 (m-90) REVERT: A 457 CYS cc_start: 0.3917 (OUTLIER) cc_final: 0.3393 (p) REVERT: A 550 LYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5406 (pttm) REVERT: B 113 ARG cc_start: 0.3677 (ttm170) cc_final: 0.1407 (tpt-90) REVERT: B 467 LEU cc_start: 0.6020 (tp) cc_final: 0.5326 (pp) REVERT: B 474 PHE cc_start: 0.4926 (OUTLIER) cc_final: 0.4597 (p90) REVERT: B 572 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7285 (mm) REVERT: C 219 ASN cc_start: 0.7197 (t0) cc_final: 0.6699 (t0) REVERT: C 332 LYS cc_start: 0.8132 (tptt) cc_final: 0.7656 (tptt) REVERT: C 358 TYR cc_start: 0.1830 (OUTLIER) cc_final: 0.1073 (p90) REVERT: H 110 MET cc_start: 0.7343 (ppp) cc_final: 0.6987 (ppp) REVERT: I 117 TYR cc_start: 0.2341 (OUTLIER) cc_final: 0.0345 (t80) REVERT: I 595 LYS cc_start: 0.3895 (OUTLIER) cc_final: 0.3391 (tttt) REVERT: I 661 VAL cc_start: 0.8853 (t) cc_final: 0.8574 (p) REVERT: J 136 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6943 (mt0) REVERT: J 336 MET cc_start: 0.7770 (mtp) cc_final: 0.7143 (tpp) REVERT: J 438 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.6944 (m-30) outliers start: 57 outliers final: 41 residues processed: 255 average time/residue: 0.4046 time to fit residues: 172.1118 Evaluate side-chains 257 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 576 CYS Chi-restraints excluded: chain H residue 621 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 595 LYS Chi-restraints excluded: chain I residue 663 MET Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 364 TRP Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 438 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 268 optimal weight: 0.0070 chunk 172 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 chunk 72 optimal weight: 0.0270 chunk 179 optimal weight: 7.9990 chunk 135 optimal weight: 30.0000 chunk 276 optimal weight: 8.9990 overall best weight: 1.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.122743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.106171 restraints weight = 119767.130| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 5.22 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25099 Z= 0.123 Angle : 0.618 29.227 34469 Z= 0.295 Chirality : 0.043 0.197 3929 Planarity : 0.004 0.045 4537 Dihedral : 6.466 63.823 3895 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.88 % Favored : 90.95 % Rotamer: Outliers : 3.47 % Allowed : 27.17 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3502 helix: 1.29 (0.20), residues: 676 sheet: -1.31 (0.21), residues: 624 loop : -1.88 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP D 345 HIS 0.009 0.001 HIS C 199 PHE 0.029 0.001 PHE J 198 TYR 0.016 0.001 TYR B 495 ARG 0.004 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 742) hydrogen bonds : angle 5.53187 ( 2037) metal coordination : bond 0.01139 ( 56) metal coordination : angle 5.62893 ( 72) SS BOND : bond 0.00488 ( 2) SS BOND : angle 0.84291 ( 4) covalent geometry : bond 0.00273 (25041) covalent geometry : angle 0.56223 (34393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15754.81 seconds wall clock time: 271 minutes 22.40 seconds (16282.40 seconds total)